Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

Rossi, Giulia; Monticelli, Luca; Puisto, S. R.; Vattulainen, Ilpo; Ala-Nissilä, Tapio

doi:10.1039/c0sm00481b

Cited by 233 publications

(334 citation statements)

References 52 publications

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“…59,60 In the MARTINI model, the molecule is described by specific interaction centers: on average one interaction center describes four non-hydrogen atoms. Such coarse-graining of the interactions allows us to study larger systems and longer 6 timescales with the same computational effort than in full atomistic detail.…”

Section: Coarse-grained Simulationsmentioning

confidence: 99%

Controlling Carbon-Nanotube—Phospholipid Solubility by Curvature-Dependent Self-Assembly

2015

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Control of aqueous dispersion is central in the processing and usage of nanoscale hydrophobic objects. However, selecting dispersive agents based on the size and form of the hydrophobic object and the role of coating morphology in dispersion efficiency remain important open questions. Here, the effect of the substrate and the dispersing molecule curvature, as well as, the influence of dispersant concentration on the adsorption morphology are examined by molecular simulations of graphene and carbon nanotube (CNT) substrates with phospholipids of varying curvature as the dispersing agents. Lipid spontaneous curvature is increased from close to zero (effectively cylindrical lipid) to highly positive (effectively conical lipid) by studying double tailed dipalmitoylphosphadidylcholine (DPPC) and single tailed lysophosphadidylcholine (LPC) which differ in the number of acyl chains but have identical head group.We find that lipids are good dispersion agents for both planar and curved nanoparticles and induce a dispersive barrier non-size selectively. Differences in dispersion efficiency arise from lipid head group density and their extension from the hydrophobic substrate in the adsorption morphology. We map the packing morphology contributing factors and report that the aggregate morphologies depend on the competition of interactions rising from 1) hydrophobicity driven maximization of lipid-substrate contacts and lipid self-adhesion, 2) tail bending energy cost, 3) preferential alignment along the graphitic substrate principal axes, and 4) lipid head group preferential packing.Curved substrates adjust the morphology by changing the balance between the interaction strengths. Jointly, the findings show substrate curvature and dimensions are a way to tune lipid adsorption to desired, self-assembling patterns. Besides engineering dispersion efficiency, the findings could bear significance in designing materials with defined molecular scale, molecular coatings for orientation specific CNT assembly or lipid-based molecular masks and patterning on graphene.2

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Section: Coarse-grained Simulationsmentioning

confidence: 99%

Controlling Carbon-Nanotube—Phospholipid Solubility by Curvature-Dependent Self-Assembly

2015

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“…All MD simulations were performed in the NPT ensemble with 300 K and 1 bar constant. The MD parameters can be seen in [5,13]. The simulations of cis-PI in solvents and melts were run for 1.5 and 6 µs, respectively.…”

Section: Coarse-grained (Cg) Modelmentioning

confidence: 99%

“…Therefore, some efforts were put to provide the more simplified representations of polymer molecules, namely the MARTINI force field [1]. The MARTINI models were built for amino acids, water, phospholipid cell membranes, fullerenes and some other polymers [2][3][4][5], but there is no parameter for rubber molecules yet. In this study, CG model of cis-PI chains were parameterized based on MARTINI scheme [1].…”

Section: Introductionmentioning

confidence: 99%

Transferability of Polymer Chain Properties between Coarse-Grained and Atomistic Models of Natural Rubber Molecule Validated by Molecular Dynamics Simulations

Kitjanon

Khuntawee

Sutthibutpong

et al. 2017

J. Phys.: Conf. Ser.

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Abstract. In this study, we have successfully parameterized the coarse-grained (CG) model of cis-1,4-polyisoprene (main component of natural rubber) based on the MARTINI force field. An isoprene monomer is mapped into one bead of CG model. The structure, bulk and thermodynamics properties of cis-1,4-polyisoprene with new CG model are well comparable to the atomistic simulation model and experiment. Our CG model of cis-1,4-polyisoprene will be helpful to study in the advanced rubber nanocomposite materials. IntroductionRubber is one of the most important natural resources and has a very high impact on Thailand's economy. It is composed mainly of high molecular weight polymer cis-1,4-polyisoprene (cis-PI). Computer simulations can play role in the advanced rubber technologies as the virtual experiments, carried out in silico, to observe and fine-tune the chemical details of both rubber and rubber composites. These numerical experiments can greatly reduce time and cost from trial and error processes in the laboratories. However, there are still rooms for improvement as the traditional detail-riched atomistic model of polymers are still consuming a large amount of computer time to produce the well-equilibrated conformation of polymer networks. Therefore, some efforts were put to provide the more simplified representations of polymer molecules, namely the MARTINI force field [1]. The MARTINI models were built for amino acids, water, phospholipid cell membranes, fullerenes and some other polymers [2][3][4][5], but there is no parameter for rubber molecules yet. In this study, CG model of cis-PI chains were parameterized based on MARTINI scheme [1]. Solvation free energy and chain properties of cis-PI were calculated in water, cyclohexane and in own melt-state. A series of molecular dynamics (MD) simulations of CG model were performed in comparison with the united-atom(UA) model to verify the transferability between two length scales.

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“…Additionally, the densities of both DMP and PPE (degree of polymerization DP=20) are used as the target to adjust the set of non-bonded parameters. [32,33]. In contrast to the 9-6 model for PPE, a standard Lennard Jones 12-6 potential function (Eq.4) is used for PS and shifted as is customary for Martini.…”

Section: Scheme 1 the Cg Mapping Of A Ppe Unitmentioning

confidence: 99%

“…A standard CG model for polymers, lipids and other molecules of biological interest is the MARTINI model [27][28][29][30][31], and this model has been extended to polymers like PS, [32,33] poly(ethylene glycol) [34], poly(ethylene oxide) and dendrimers [35] etc. Benzene rings are modelled by three beads in the MARTINI approach.…”

Section: Introductionmentioning

confidence: 99%

Refinement of a coarse-grained model of poly(2,6-dimethyl-1,4-phenylene ether) and its application to blends of PPE and PS

Wang

Shentu

Faller

2015

Molecular Simulation

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Abstract:A coarse-grained (CG) molecular simulation model has been refined for poly (2,6-dimethyl-1,4-phenylene ether) (PPE). This was successfully validated against atomistic simulation and experimental data. Particularly, the glass transition temperature (T g ) of PPE was studied using both atomistic and CG models and compared favorably to experimental data. In addition, we used the CG model together with an existing Martini CG model of polystyrene (PS) to study the blending behavior of these two polymers. We solved the problem to mix the different potentials and molecular dynamics of high-molecular-weight blends of PPE/PS was performed in detail.

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Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

Cited by 233 publications

References 52 publications

Controlling Carbon-Nanotube—Phospholipid Solubility by Curvature-Dependent Self-Assembly

Controlling Carbon-Nanotube—Phospholipid Solubility by Curvature-Dependent Self-Assembly

Transferability of Polymer Chain Properties between Coarse-Grained and Atomistic Models of Natural Rubber Molecule Validated by Molecular Dynamics Simulations

Refinement of a coarse-grained model of poly(2,6-dimethyl-1,4-phenylene ether) and its application to blends of PPE and PS

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